During peak-hour, Geelong trains are at up to 140 per cent capacity, mainly along the outer-western suburb stations that were added as part of the rail link.

It means 12 of the 16 morning peak trains are more than 100 per cent full, well before they reach Southern Cross Station.

Geelong trains are at up to 140 per cent capacity during peak hour. Photo: Joe Armao

Across the board, V/Line passengers are enduring delays, cancellations and overcrowding.

Nearly one in three V/Line trains are over capacity and close to 90 per cent are running late, according to a report from the Deputy Auditor General.

The Regional Rail Link effectA sharp 18.3 per cent increase in overall passenger numbers between 2014 and 2016 has been largely attributed to the rail link, which was designed to help V/Line services cope with the booming population in the western corridor, in suburbs like Tarneit and Wyndham Vale. The Regional Rail Link, on which Bendigo and Ballarat trains also run, was also intended to ease congestion on tracks shared with Metro Rail trains.

Seats are a premium on V/Line services. Photo: Joe Armao"V/Line has not successfully dealt with the challenges it has faced over the past decade," he said.

"V/Line was not prepared for the strong growth in patronage and the resulting increase in service demand following the opening of the [Regional Rail Link], which fundamentally changed the nature of its operations."

Mr Barry highlighted a serious asset management problem at V/Line, which has resulted in a maintenance backlog it estimates could cost $534.8 million to manage.

But he said V/Line was starting to turn the situation around.

In a shift that is likely to raise the ire of regional rail commuters, Mr Barry said V/Line was adopting a more "commuter-style" service.

"V/Line is modifying new trains, including increasing seating, and is also preparing for more services with customers standing for part or all of the journey," he said.

"This will require a significant shift in V/Line passengers' expectations, especially for those who have historically experienced adequate seating availability."

V/Line has already added handles to seats on VLocity trains for standing passengers.

Punctuality problemsThere is an inability to consistently get V/Line trains to arrive at the metropolitan boundary in time, Mr Barry found. In 2014-15, nearly 90 per cent of V/Line trains reached the city boundary up to three minutes late.

"V/Line advised this is mainly due to congestion in the metropolitan area, which limits the paths available to V/Line services and requires its trains to run at slower speeds," he said.

Factors leading to punctuality problems include: excessive wheel wear in VLocity trains, the failure of VLocity trains to activate boom gates on time, and congestion on the shared metropolitan networks.

Minister for Public Transport Jacinta Allan said the service had shown recent improvements "after years of cuts and neglect from the former Liberal and National government".

"We've added nearly 600 new services, and are getting on with the Regional Rail Revival, which will improve every regional passenger line in the state – allowing more trains, more often, across regional Victoria."

Shadow Minister for Public Transport David Hodgett said under the Labor government, "regional Victoria is treated as second rate compared to Melbourne".